Rye ( Secale cereale L.) belongs to the Triticeae tribe, along with other economically important cereals such as wheat and barley. Overall, our study successfully demonstrates the high prospective impact of comparing genetic diversity and structure of cultivars, ex situ, and in situ samples in ascertaining the status of plant genetic resources (PGR). Such genetic distinctiveness of in situ accessions highlights their unexplored potential as new genetic resources, which can be used to boost rye breeding strategies and the production of new varieties. Rye genetic diversity and population structure analysis does not present any geographical trend but disclosed marked differences between genetic backgrounds of in situ accessions and those of cultivars/ ex situ collections. Here, we perform the first comprehensive assessment of rye's genetic diversity and population structuring using cultivars, ex situ landraces along a comprehensive sampling of in situ accessions from Portugal, through a molecular-directed analysis using SSRs markers. Thus evaluation of in situ populations is of utmost importance to unveil “on farm” diversity, which is largely undervalued. Previous studies on rye's genetic diversity revealed moreover a common genetic background on landraces ( ex situ) and cultivars, regardless of breeding level or geographical origin. Such narrowing of rye genetic diversity results from the presence of “Petkus” pool in most modern rye varieties as well as “Petkus” × “Carsten” heterotic pool in hybrid rye breeding programs. Rye ( Secale cereale L.) is a cereal crop of major importance in many parts of Europe and rye breeders are presently very concerned with the restrict pool of rye genetic resources available. 4Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.3Plant Biology/Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal.2Colégio F3 Food, Farming and Forestry, Universidade de Lisboa, Lisboa, Portugal.1Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal.Filipa Monteiro 1 *, Patrícia Vidigal 1, André B.
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